5LVH | pdb_00005lvh

Hen Egg White Lysozyme co-crystallized with trans-Ru(DMSO)4Cl2

PDB DOI: https://doi.org/10.2210/pdb5LVH/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Expression System: Gallus gallus
Mutation(s): No

Deposited: 2016-09-14 Released: 2016-09-21
Deposition Author(s): Kurpiewska, K., Halajko, P., Lewinski, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.210 (Depositor), 0.216 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Ligand-dependent interaction of anticancer ruthenium complexes with hen egg white lysozyme and human lysozyme

Oszajca, M., Kurpiewska, K., Halajko, P., Szura, A., Lewinski, K., Brindell, M.

To be published.

Macromolecule Content

Total Structure Weight: 15.04 kDa
Atom Count: 1,213
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0 Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RU Query on RU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain E [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.210 (Depositor), 0.216 (DCC)
R-Value Work: 0.171 (Depositor), 0.182 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.683	α = 90
b = 77.683	β = 90
c = 37.195	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Kurpiewska, K.

Halajko, P.

Lewinski, K.

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary